The Human Genome Sequence Is not Complete

 
The latest version of the human genome sequence is called Build 36 or GRCh37. Here's an overview from the Genome Reference Consortium.


The large red triangles represent regions where there is a lot of variability so that no single representation of the genome sequence will describe a majority of humans.

The black regions represent parts of the chromosomes that have not been sequenced and assembled into long stretches (contigs) of reliable sequence. Most of the unsequenced regions are at centromeres, or telomeres, or on the Y chromosome. These regions consist of thousands of copies of highly repetitive DNA. It is impossible to assemble these repetitive sequences.

Scientists are urging that more attention be focused on completing the chimpanzee and macaque genome sequences. We have been waiting a long time for the draft sequences of those genomes to be finished. The explosion of data on the human genome can only be realistically evaluated by comparing it to our closest relatives. (For example, are human non-coding RNAs conserved in primates?)

The fact that the human genome is not complete is not a problem. We know what's in the repetitive sequence regions even though we don't know exactly how it is arranged. The effort required to finish of the last bit is probably not as important as getting a final draft of other sequences.

Sandra Porter wonders Why don't we finish the human genome first?.

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Jason Rosenhouse Doesn't Understand Pluralists

 
Jason Rosenhouse has posted some comments on a recent book review by Richard Lewontin. In that book review, Lewontin—who along with Gould is the co-author of the spandrels paper—questions the emphasis on natural selection and the use pf "Darwinism" as a synonym for evolution. Read Lewontin on Darwin to see what Jason thinks of the book review.

I want to focus on a specific question that Jason Rosenhouse asks.

I've never really understood what it is exactly that anti-selectionists are complaining about. If they agree that complex adapations arise as the result of gradual accretion mediated by natural selection, then I fail to see how they are really so different from people like Richard Dawkins or Daniel Dennett (two people often described as being beknighted uber-selectionists). If they do not agree then I would like to hear their proposed alternative mechanism.

The original paper by Gould and Lewontin, The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme, explains the problem very well. The authors begin their criticism with ...

We wish to question a deeply engrained habit of thinking among students of evolution. We call it the adaptationist programme, or the Panglossian paradigm. It is rooted in a notion popularized by A.R. Wallace and A. Weismann, (but not, as we shall see, by Darwin) toward the end of the nineteenth century: the near omnipotence of natural selection in forging organic design and fashioning the best among possible worlds. This programme regards natural selection as so powerful and the constraints upon it so few that direct production of adaptation through its operation becomes the primary cause of nearly all organic form, function, and behavior. Constraints upon the pervasive power of natural selection are recognized of course (phyletic inertia primarily among them, although immediate architectural constraints, as discussed in the last section, are rarely acknowledged). But they are usually dismissed as unimportant or else, and more frustratingly, simply acknowledged and then not taken to heart and invoked.

The anti-selectionists—I am one—do not question the fact that adaptations are produced by natural selection. What we question is whether everything in evolution is an adaptation. We question those who think that "evolution" and "natural selection" are synonyms. And since "Darwinism" is equivalent to evolution by natural selection we question whether evolution is the same as Darwinism.

We pluralists like to point out that much of evolution is due to random genetic drift. Since Darwin's name is not associated with the theory of evolution by random genetic drift, it is inappropriate to say that all of evolution is Darwinist.

It's not that complicated. It was all explained in the classic spandrels paper published 30 years ago. Complex biological structures may be due entirely to adaptation, or they may be mostly an accident that's arisen by random genetic drift, or they may be due to combinations of drift and selection.

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What do protein crystallographers dream of?

 
"What do protein crystallographers dream of?" is the question asked by Ananyo Bhattacharya in an article published in Nature [Protein structures: Structures of desire].

The structures of many protein complexes have been determined but crystallographers have a list of holy grails that, so far, have eluded them. It's an interesting list and one that I mostly agree with. Can you identify the structure shown here in cartoon form?

One glaring omission is pyruvate dehydrogenase. Lot's of people want to see that structure. Other notable omissions include complex I of the membrane-associated electron transport chain and the protein import complex of the endoplasmic reticulum. Don't protein crystallographers dream of those?

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The Biology Textbooks Are Wrong?

 
The other day I suggested that Casey Luskin was probably just ignorant. Unlike other creationists, he problably isn't a liar. Today I'm not so sure.



What is it with FOX news?

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Win Free Prizes from Denyse O'Leary

 
Every week there are dozens of people who try to guess Monday's Molecule and win a free lunch with me. Now, that's a valuable prize—it's no wonder that so many people are trying to win.

Now you've got another chance to win valuable prizes. Denyse O'Leary is giving out prizes for people who comment on Uncommon Descent [Earn free stuff!: The Uncommon Descent Contest].

What are the prizes?

• 10 DVDs of Expelled,courtesy the producers.
• 10 DVDs of Privileged Planet, courtesy the producers.
• 5 subscriptions, including back issues, to the excellent Christian/theistic science and culture mag, Salvo, complete with recent back issues, courtesy the editor-in-chief.

Looks like I've got serious competition!

Here's the first contest question: Does the multiverse help science make sense - or simply destroy science?. Hmmm ... I wonder what the right answer is?

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Casey Luskin Writes About the Universal Common Ancestor

 
Casey Luskin is writing about the tree of life and the universal common ancestor. The second installment in a series of five posting is here.

When speaking to the public, evolutionists are infamous for overstating the evidence for universal common ancestry. For example, when speaking before the Texas State Board of Education in January, 2009, University of Texas evolutionist biologist David Hillis cited himself as one of the “world’s leading experts on the tree of life” and later told the Board that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence” when reconstructing evolutionary history using biological molecules. But this is not accurate. Indeed, in the technical scientific literature, one finds a vast swath of scientific papers that have found contradictions, inconsistencies, and flat out failures of the molecular data to provide a clear picture of phylogenetic history and common descent.

Indeed, the cover story of the journal New Scientist, published on the very day that Dr. Hillis testified, was titled, “Why Darwin was wrong about the tree of life.” Directly contradicting Hillis’ gross oversimplification of molecular systematics, the article reported that “The problem was that different genes told contradictory evolutionary stories.” The article observed that with the sequencing of the genes and proteins of various living organisms, the tree of life fell apart:

It's true that things are very confusing at the base of the tree of life. The evidence indicates that genes were frequently exchanged between primitive prokaryotic species and this means there is no single tree that represents all of life.

But this doesn't negate the idea of a universal common ancestor. The origin of life could still be a unique event that gave rise over millions of years to many different descendants that subsequently exchanged genes. Or, there may have been a few independent origins of life.

The available evidence shows that most fundamental properties of life are shared by all living things (e.g. basic metabolic pathways, genetic code). This is consistent with a unique origin of life but it's also consistent with multiple origins as long as only one version of each process has survived. The odds favor a single origin and a universal common ancestor.

What's interesting about Luskin's article is that he is hopelessly confused about the difference between a phylogenetic tree and the origin or life. He seems to think that a bushy tree with many interconnecting branches rules out a universal common ancestor. I don't know what he postulates in its place unless the idea of God creating three or four different primitive prokaryotes is what appeals to him more than God just doing it once.

Intelligent Design Creationists come in many different flavors. Often it's hard to decide whether they are being deceptive (lying) or just ignorant. I think that Casey Luskin is just ignorant. He finds it difficult to make a coherent argument and he doesn't take the time to learn more about his subject. In that sense, he's much less dangerous than Jonathan Wells.

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Call a Canadian!!

 
Dear Americans,

Have you ever thought about asking an average Canadian what they think of their health care system? Read Call a Canadian on Effect Measure.

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Oops! Did New Scientist Goof Again?

 
New Scientist published an article on Science and art: Still two cultures divided?.

The journal invited six people to comment on the two cultures. Here's the list ....

• Stefan Collini is a professor of literature and intellectual history at the University of Cambridge. He edited The Two Cultures (1993, CUP)
• Susan Haack is a professor of philosophy and a professor of law at the University of Miami, Florida
• Harry Collins is professor of sociology at Cardiff University in the UK
• Mary Midgley is a philosopher and writer
• Sandra Harding is a philosopher and professor of education at the University of California, Los Angeles
• A. C. Grayling is a professor of philosophy at Birkbeck, University of London

A perceptive commenter (Khoo) asks, "Why was an entire article written about the divide between the arts and the sciences, and not a single physical scientist or mathematician interviewed? Does the author believe these scientists have nothing to say about the arts?"

Good point. A classic demonstration of the two cultures in action.

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Atheists Serve the Devil!

 

Who knew? I wonder what the Devil eats for lunch? If I'm going to serve him I'd better find out.

Is he a big tipper?

This is Pat Robertson responding to a question. A caller wants to know how she, a Christian, can get along with her boyfriend, an atheist. Can you guess how the good Christian responds? Think about it, then watch.

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[Hat Tip: Friendly Atheist]

How to Frame a Null Hypothesis

A reader has alerted me to an article by Michael White at Adaptive Complexity: Genomic Junk and Transcriptional Noise.

With hot, new technologies, biologists are taking higher-resolution snapshots of what's going on inside the cell, but the results are stirring up controversy. One of the most interesting recent discoveries is that transcription is everywhere: DNA is transcribed into RNA all over the genome, even DNA that has long been thought to have a non-functional role. What is all of this transcription for? Does the 'dark matter' of the genome have some cryptic, undiscovered function?

Unfortunately, in all of the excitement over possible new functions, many biologists have forgotten how to frame a null hypothesis - the default scenario that you expect to see if there is no function to this transcribed DNA. As a result, the literature is teeming with wild, implausible speculation about how our excess DNA might be beneficial to us.

So here, let's step back and look at what we expect from DNA when it's playing absolutely no functional role; in other words, let's look at the null hypothesis of genomic junk and transcriptional noise. We can then take our null hypothesis and use it to look at a fascinating new study of how genomic parasites sculpt transcription in our cells.

If you are interested in what's wrong with science these days then you must read his article.

The point is not whether you believe that all transcription is adaptive and functional, or whether you believe that most of it is noise. The real point is that it is very bad science to ignore the null hypothesis and publish naive speculation as if it were the only possible explanation.

Whenever you see a paper that fails to address the null hypothesis you can be sure that you are reading bad science. Everything else in the paper is suspect.

The key fact that most scientists are overlooking is that RNA polymerase and the various transcription factors must bind non-specifically at thousands of sites in a random sequence of junk DNA. This is just basic biochemistry of the sort that should be taught in undergraduate classes. Transcription will be initiated by accident at some of these sites even though they are not functional promoters. Again, this is basic biochemistry.

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[Image Credit: Horton et al. Principles of Biochemistry 4/e p.657]

Two Cultures in New York City

 
Tomorrow is the 50th anniversary of a lecture by C.P. Snow on The Two Cultures.

He said,

A good many times I have been present at gatherings of people who, by the standards of the traditional culture, are thought highly educated and who have with considerable gusto been expressing their incredulity at the illiteracy of scientists. Once or twice I have been provoked and have asked the company how many of them could describe the Second Law of Thermodynamics, the law of entropy. The response was cold: it was also negative. Yet I was asking something which is about the scientific equivalent of: 'Have you read a work of Shakespeare's?'

I now believe that if I had asked an even simpler question — such as, What do you mean by mass, or acceleration, which is the scientific equivalent of saying, 'Can you read?' — not more than one in ten of the highly educated would have felt that I was speaking the same language. So the great edifice of modern physics goes up, and the majority of the cleverest people in the western world have about as much insight into it as their Neolithic ancestors would have had.

Not much has changed in fifty years. We still live in a society that is at best scientifically illiterate and, at worst, anti-science.

Tomorrow I'll be on my way to New York City to attend a conference on The Two Cultures in the 21st Century. The meeting was organized (in part) by Chris Mooney and Sheril Kirshenbaum. It begins with a keynote address by E.O. Wilson followed by four symposia on ...

• The Two Cultures in Historical Perspective: From Aristotle to "Science Wars" and the "Third Culture"
• How to More Effectively Communicate Science Issues to the Public
• Restoring Science to Its Rightful Place in Politics
• A Better Future through Science Citizenship

Carl, (I Got Your Two Cultures Right Here), Zimmer will be there.

We all have our stories and our examples of the problem. The one I like to tell is the story about a group of knowledgeable adults at a cocktail party when something mathematical comes up in the conversation. Chances are someone is going to brag about how much they feared math in schools and how little they know about the subject. This will undoubtedly get murmurs of sympathy from many people.

Now imagine that the group was discussing modern literature and I said something similar; "I hated literature in school, I never 'got' the point of these modern writers and why they are so famous. Literature was way too hard for me so I stopped taking literature courses as soon as I could." Do you think there would be murmurs of sympathy and understanding? I doubt it. The group would probably think I'm stupid.

The two cultures problem will only be solved when the proper response to someone who claims to be an idiot in mathematics is the same as to someone who claims to be an idiot about art and literature.

The other problem is when people claim to be knowledgeable about science when they aren't. Chris Matthews of MSNBC has the right idea when he attacks Rep. Mike Pence (Indiana-R) ["You Want to Educate Americans About Science; Do You Believe In Evolution?"]. We can't allow people to pretend they know about science when they reject the core principles of science. If you are ignorant about science then you are ignorant, period.

Today's issue of New Scientist has an article on Science and art: Still two cultures divided? .

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On the Origin of Chloroplasts

 
We know that many species contain chloroplasts. In most cases, these species descend directly from a common ancestor that acquired the chloroplast through an endosymbiotic relationship with a cyanobacterium. The endosymbiotic origin of chloroplasts from cyanobacteria is not in doubt.

What is in doubt is whether the original endosymbiosis happened just once or whether there are multiple independent origins of chloroplasts. We also know that some species acquired chloroplasts by fusing with another chloroplast-containing eukaryotic species. How many examples of secondary acquisition are required to explain the phylogeny of species that contain chloroplasts? Are there tertiary and quaternary acquisitions?

Christopher Taylor of Catalogue of Organisms has posted a nice summary of the problems in this field at Crossing the Algal Divide. If you want to keep up with one of the important problems in evolution then this is an excellent place to start.

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[Photo Credit: micro*scope]

Monday's Molecule #120: Winners

 
UPDATE: The image depicts the genome of a human papillomavirus. The Nobel Laureate is Harald zur Hausen.

This week's winners are Dima Klenchin of the University of Wisconsin and Adam Santoro of the University of Toronto. They were the first of many who got the right answer. This surprises me 'cause I thought it would be harder. I didn't realize how easy it was to get the molecule by searching for "E6" or "E7."

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This is a cartoon showing the genes present in a particular DNA molecule. Your task is to identify the kind of DNA molecule being depicted.

There is one Nobel Laureate who is most closely identified with this particular type of molecule. You have to identify the Nobel Laureate and what the prize was for.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are six ineligible candidates for this week's reward: Shumona De of Dalhousie University, Maria Altshuler of the University of Toronto, Mike Fraser of Toronto, Alex Ling of the University of Toronto, Laura Gerth of the University of Notre Dame, and Stefan Tarnawsky of the University of Toronto.

The Canadians continue their total dominance of the rest of the world. That's as it should be.

I still have one extra free lunch donated by a previous winner to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours. Comments are now open.

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How to Teach Evolution?

 
You're not going to believe this. The National Institute of General Medical Sciences (NIGMS), the Office of Science Education (OSE), and the National Academy of Sciences (NAS) sponsored Matt Nisbet to give a lecture on Communicating About Evolution.

Who knew that Matt was an expert on evolution? Here's what Matt says about the lecture on his website [Video for NAS Lecture: Communicating about Evolution].

For readers of this blog and followers of the "Framing Science" thesis, the National Academies presentation is the most detailed lecture I have given on how to effectively engage with the public on the relationship between science and religion and the specific topic of evolution. The lecture follows closely articles and book chapters that I have previously published or that are forthcoming.

Near the end of his lecture Matt defends the "frame" of emphasizing that religion and science are not in conflict (~50 minutes). In this context, frame is not much different than spin and spin is not much different than lie. The truth is that science and religion are often in conflict. Any statement to the contrary is not the truth.

Matt's views about framing have been so thoroughly rejected by scientists that The National Institute of General Medical Sciences (NIGMS), the Office of Science Education (OSE), and the National Academy of Sciences (NAS) should be ashamed of themselves.

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See Matt Nisbet Endorses Francis Collins for Presidential Science Advisor - The Kiss of Death for an example of how Nisbet wants to frame the debate.

Do High School Student Want to Become Scientists?

 
Do High School Student Want to Become Scientists? the answer is, no [Is Canada losing the lab-rat race?].

"Look up 'scientist' on Google," the 16-year-old says, "and you will see someone in a lab coat." At the moment, she is considering something with more immediate results, such as physiotherapy.

Ask her biology classmates at Colonel By Secondary School in Ottawa if any of them want to be scientists and only a few tentative hands flicker up. What's worrying is that this is no average high-school science class. It is part of the International Baccalaureate program, chosen from a large pool of applicants. These are students who spend half of their time in labs, working through experiments, not dozing off during lectures - the kind of education most scientists wish they had had. If any group should be producing lab-coat keeners, it should be this one.

Julia Dutaud, 16, sitting in the back in her school-rugby T-shirt, would like to study environmental science - a field growing as rapidly as any - but she wonders if she could make a good living at it: "Going into science would be a nice thing to do," she says. "But we aren't sure how much opportunity we would get after university."

Half the students are planning to be doctors instead, a profession they and their parents consider more stable.

I don't think this is a new problem. Back in the olden days, there also weren't a huge number of high school students who wanted to be scientists. Why should there be a significant number in a typical high school class? At my university there are about 8,000 students entering first year and about 400 or so want to pursue a career in science. That's about right—half of them (200) will be able to enter graduate school when they graduate and that's also about right. It means that a typical high school science class of 25 students will likely have only two or three who want to be scientists.

It would be a disaster if half of every high school science class wanted to become scientists because the vast majority would be disappointed.

There's another problem not covered in the Globe and Mail article. In my experience, many students don't begin to understand what a scientist is until they get to university and start seeing them in their natural environment. A surprising number of high school students think you have to be a physician in order to do the cool research on genes and diseases. It's only after they get to university that they learn the difference between a physician and a scientist.

When did you, dear reader, first develop a serious interest in science? Was it in high school or university? Is it a problem that there aren't more high school students who want to become scientists?

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